Phytase enzymes are a group of histidine acid phosphatases with great potential for improving mineral nutrition and protecting the environment from phosphorus pollution coming from animal waste (Lei et al., J. Appl. Anim. Res. 17:97-112 (2000)). Aspergillus niger NRRL 3135 phyA phytase has been cloned (Mullaney et al., “Positive Identification of a Lambda gt11 Clone Containing a Region of Fungal Phytase Gene by Immunoprobe and Sequence Verification,” Appl. Microbiol. Biotechnol. 35:611-614 (1991); and Van Hartingsveldt et al., “Cloning, Characterization and Overexpression of the Phytase-Encoding Gene (phyA) of Aspergillus niger,” Gene 127:87-94 (1993)) and overexpressed for commercial use as animal feed additive (Van Dijck, J. Biotechnology 67:77-80 (1999)). Recent information on its molecular structure from its X-ray-deduced three dimensional structure (Kostrewa et al., “Crystal Structure of Phytase from Aspergillus ficuum at 2.5 Å Resolution,” Nat. Struct. Biol. 4:185-190 (1997)) has facilitated several studies to enhance the specific activity of other phytases. In one of these studies, a recombinant A. fumigatus ATCC 13070 phytase had its specific activity with phytic acid as substrate significantly enhanced by the replacement of glutamine (Q) at position 27 for leucine (L). It was suggested that amino acid (“AA”) residue 27 was part of the active site in A. fumigatus phytase (Tomschy et al., “Optimization of the Catalytic Properties of Aspergillus fumigatus Phytase Based on the Three-Dimensional Structure,” Protein Science 9:1304-1311 (2000)). The presence of leucine at this AA residue in A. terreus phytase (Mitchell et al., “The Phytase Subfamily of Histidine Acid Phosphatases: Isolation of Genes for Two Novel Phytases From the Fungi Aspergillus terreus and Myceliophthora thermophila,” Microbiology 143:245-252 (1997)) also supports this replacement of glutamine with leucine, since A. terreus phytase displays even higher activity than A. niger NRRL 3135 phytase (Wyss et al., “Biochemical Characterization of Fungal Phytases (myo-inositol hexakisphosphate phosphohydrolases): Catalytic Properties,” Appl. Environ. Microbiol. 65:367-373 (1999)). The replacement of Q with L was theorized as resulting in the elimination of a hydrogen bond between the side chain of Q and the 6-phosphate group of myo-inositol hexakisphosphate. This bond was postulated to be a reason for the lower specific activity of A. fumigatus ATTC 13070 phytase. Substitution of proline at residue 27 resulted in lower activity than the wild type enzyme. However, it was noted in that study that the proline substitution mutant phytase displayed a tendency to aggregate and precipitate and this could have lowered its true activity level. A. niger NRRL 3135 phytase like A. fumigatus phytase has Q at AA residue 27, and it remains to be determined how specific activity responds to substitutions of Q27L and Q27P.
Phytase from Aspergillus fumigatus has been studied for its good thermotolerance properties, significant levels of activity over a wide range of pH, and resistance to hydrolysis by pepsin (Pasamontes et al., “Gene Cloning, Purification, and Characterization of a Heat-Stable Phytase From the Fungus Aspergillus fumigatus,” Appl. Environ. Microbiol. 63:1696-1700 (1997); and Rodriguez et al., “Expression of the Aspergillus fumigatus Phytase Gene in Pichia pastoris and Characterization of the Recombinant Enzyme,” Biochem. Biophys. Res. Commun. 268:373-378 (2000)). However, specific activity of this phytase is not as high as some other fungal phytases such as those produced by A. terreus or A. niger. 
During the last decade, the increased use of plant proteins such as soybean meal, etc., in animal feed (Berlan et al., “The Growth of the American ‘Soybean Complex’,” Eur. R. Agr. Eco. 4:395-416 (1977)) has created an expanding market for phytase as an animal feed additive. Adding phytase allows monogastric animals, i.e., poultry and swine, to utilize the phytin phosphorus in this plant meal (Mullaney et al., “Advances in Phytase Research,” Advances in Applied Microbiology 47:157-199 (2000)). Without phytase, the phytin bound phosphorus is unavailable to these animals and is excreted in their manure where it can potentially harm the environment by further elevating the soil phosphorus levels (Wodzinski et al., “Phytase,” Advances in Applied Microbiology 42:263-302 (1996)). During this period, the phytaseA gene (phyA) from Aspergillus niger (ficuum) NRRL 3135 was cloned, overexpressed, and its product marketed as (Natuphos®) in the animal feed industry as an effective means to lower phosphate levels in manure from poultry and swine (van Hartingsveldt et al., “Cloning, Characterization and Overexpression of the Phytase-Encoding Gene (phyA) of Aspergillus niger,” Gene 127:87-94 (1993)).
The native NRRL 3135 phyA phytase is a stable enzyme (Ullah et al., “Extracellular Phytase (E. C. 3.1.3.8) from Aspergillus ficuum NRRL 3135: Purification and Characterization,” Prep. Boichem. 17:63-91 (1987)) that has a high specific activity for phytic acid (Wyss et al., “Biochemical Characterization of Fungal Phytases (Myo-inositol Hexakisphosphate Phosphohydrolases): Catalytic Properties,” Applied and Envir. Micro. 65:367-373 (1999)). This has contributed to its acceptance by the animal feed industry (Wodzinski et al., “Phytase,” Advances in Applied Microbiology 42:263-302 (1996)). It has also been widely researched and utilized to engineer improved features into other fungal phytases by recombinant DNA techniques (Wyss et al., “Biophysical Characterization of Fungal Phytases (Myo-iositol Hexakisphosphate Phosphohydrolases): Molecular Size, Glycosylation Pattern, and Engineering of Proteolytic Resistance,” Applied and Envir. Micro. 65:359-366 (1999); and Lehmann et al., “Exchanging the Active Site Between Phytases for Altering the Functional Properties of the Enzyme,” Protein Science 9:1866-1872 (2000)). However, to date no studies have successfully employed any of this information to improve this widely used benchmark phytase.
NRRL 3135 PhyA is known to have an active site motif characteristic of the histidine acid phosphatase (HAP) class of enzymes (Ullah et al., “Cyclohexanedione Modification of Arginine at the Active Site of Aspergillus ficuum Phytase,” Biochem. Biophys. Res. Commun. 178:45-53 (1991); and Van Etten et al., “Covalent Structure, Disulfide Bonding, and Identification of Reactive Surface and Active Site Residues of Human Prostatic Acid Phosphatase,” J. Biol. Chem. 266:2313-2319 (1991)). Previous studies of the crystal structure of the A. niger NRRL 3135 phyA (Kostrewa et al., “Crystal Structure of Phytase from Aspergillus ficuum at 2.5 Å Resolution,” Nat. Struct. Biol. 4:185-190 (1997)) and phyB (Kostrewa et al., “Crystal Structure of Aspergillus niger pH 2.5 Acid Phosphatase at 2.4 Å Resolution,” J. Mol. Biol. 288:965-974 (1999)) molecules have provided researchers with structural models of both these enzymes. These models have facilitated the identification of the residues constituting the catalytic active center of the molecules, i.e., both the active site and substrate specificity site. Its active site consists of a catalytic center (R81, H82, R66, R156, H361 D362) and a substrate specificity site (K91, K94, E228, D262, K300, K301) (Kostrewa et al., “Crystal Structure of Aspergillus niger pH 2.5 Acid Phosphatase at 2.4 Å Resolution,” J. Mol. Biol. 288:965-974 (1999)). The amino acid numbers refer to full length phytase encoded by the A. niger NRRL 3135 phyA gene (NCBI Accession No. P34752). Amino acid reference numbers in Kostrewa et al., “Crystal Structure of Aspergillus niger pH 2.5 Acid Phosphatase at 2.4 Å Resolution,” J. Mol. Biol. 288:965-974 (1999) were derived from a slightly truncated sequence. The narrow substrate specificity and the unique pH activity profile of this phytase, a drop in activity in the pH range 3.0-5.0, have been ascribed to the interaction of these acidic and basic amino acids comprising the substrate specificity site. This low activity at this intermediate pH range is not observed in other fungal phytases and is an undesirable feature of A. niger NRRL 3135 phyA.
This information has enabled the catalytic properties of other phyAs to be altered by site-directed mutations of specific amino acids (Tomschy et al., “Optimization of the Catalytic Properties of Aspergillus fumigatus Phytase Based on the Three-Dimensional Structure,” Protein Science 9:1304-1311 (2000); Tomschy et al., “Active Site Residue 297 of Aspergillus niger Phytase Critically Affects the Catalytic Properties,” FEBS 472:169-172 (2000); and Lehmann et al., “Exchanging the Active Site Between Phytases for Altering the Functional Properties of the Enzyme,” Protein Science 9:1866-1872 (2000)). In the case of A. fumigatus, the three-dimensional structure of the native NRRL 3135 phytase molecule was utilized to identify nonconserved amino acids that were associated with increased catalytic activity (Tomschy et al., “Optimization of the Catalytic Properties of Aspergillus fumigatus Phytase Based on the Three-Dimensional Structure,” Protein Science 9:1304-1311 (2000)). In that study, the change of a single amino acid residue, Q27, had a significant effect on specific activity, pH activity profile, and substrate specificity. The critical role of a single amino acid residue, R297, was also demonstrated in A. niger T213 phyA (Tomschy et al., “Active Site Residue 297 of Aspergillus niger Phytase Critically Affects the Catalytic Properties,” FEBS 472:169-172 (2000)). A. niger T213 phyA differs from A. niger NRRL 3135 phyA in only 12 amino acid residues, but has a significantly lower specific activity for phytic acid than NRRL 3135 phytase. An analysis of the available 3D structure information identified only three divergent residues with an association with the substrate binding site. Independent site-directed mutation replacements of these three amino acids established that only R297 was responsible for strain T213's lower specific activity. Replacement of this residue with glutamine (Q), the residue at this position in A. niger NRRL 3135 phyA, resulted in a two optima pH profile and a specific activity level nearly identical with A. niger NRRL 3135 phyA. The shorter side chain of the neutral Q, which results in lower binding of substrates and products, was cited as the presumed reason for the increased specific activity in the recombinant phytase. Lehmann et al. modified the catalytic properties of a synthetic phytase, consensus phytase-1, by replacing 23 amino acids in the synthetic phytase with the corresponding amino acid in A. niger NRRL 3135 phyA (Lehmann et al., “Exchanging the Active Site Between Phytases for Altering the Functional Properties of the Enzyme,” Protein Science 9:1866-1872 (2000)). This new consensus phytase, consensus phytase-7, and A. niger NRRL 3135 phyA then had almost identical amino acids within or immediately adjacent to their active site. Consensus phytase-7 catalytic characteristics were reported to have shifted to the more favorable properties of A. niger NRRL 3135 phyA.
Phytate (myo-inositol hexakisphosphate) is the major form of phosphorus in plant origin feed. Non-ruminants such as poultry and swine are unable to utilize phytate phosphorus in soy-corn based diet. Supplemental microbial phytase has been used successfully to improve phytate phosphorus utilization and to reduce phosphorus excretion by these animals (Lei et al., “Supplementing Corn-Soybean Meal Diets with Microbial Phytase Linearly Improves Phytate Phosphorus Utilization by Weanling Pigs,” J. Anim. Sci. 71:3359-3367 (1993); and Lei et al., “Supplemental Microbial Phytase Improves Bioavailability of Dietary Zinc to Weanling Pigs,” J. Nutr. 123:1117-23 (1993)). The most widely used commercial phytase is Aspergillus niger PhyA. However, this enzyme has a unique pH profile: two pH optima, 5 to 5.5 and 2.5, a drop in activity in the range of pH 3 to 5, and a dip at pH 3.5. Because phytate degradation by dietary phytase takes place mainly in the stomach (Yi et al., “Sites of Phytase Activity in the Gastrointestinal Tract of Young Pigs,” Animal Feed Science Technology 61:361-368 (1996)), in which pH ranges from 2.5 to 3.5, the activity dip of PhyA at pH 3.5 really limits its efficacy in animal feeding.
PhyA belongs to the histidine acid phosphatase (HAP) enzyme family and has the characteristic active site motifs: RHG and HD. In general, histidine in the RHG motif is proposed to perform the nucleophilic attack, and aspartic acid in the HD motif is proposed to protonate the leaving alcohol (Ostanin et al., “Overexpression, Site-Directed Mutagenesis, and Mechanism of Escherichia coli Acid Phosphatase,” J. Biol. Chem. 267:22830-22836 (1992); Ostanin et al., “Asp(304) of Escherichia coli Acid Phosphatase is Involved in Leaving Group Protonation,” J. Biol. Chem. 268(28):20778-20784 (1993); and Kostrewa et al., “Crystal Structure of Phytase from Aspergillus ficuum at 2.5 A Resolution,” Nat. Struct. Biol. 4:185-90 (1997)). The clustering of basic amino acids at the active site of PhyA creates a favorable electrostatic environment for binding the highly negatively charged substrate phytate. Two arginine residues (81 and 85) in the RHG motif are known to bind with the scissible phosphate group of the phytate, while other amino acid residues in the α-domain are involved in the substrate binding (P87, T88, K91, K94, E228, D262, K300, K301) (Kostrewa et al., “Crystal Structure of Aspergillus niger pH 2.5 Acid Phosphatase at 2.4 Å Resolution,” J. Mol. Biol. 288:965-974 (1999)).
The pKa values of the acid/base catalysts in the catalytic active sites normally determine the pH profiles of enzyme activity (Nielsen et al., “The Determinants of—Amylase pH—Activity Profiles,” Protein Eng. 14:505-512 (2001)). Since the pKa value of a residue depends on the free energy difference between the neutral and the charged states of the residue in the protein, an enzyme pH profile may be altered by changing the charges of amino acid residues near the acid/base catalytic residues. A negatively charged amino acid generally raises the pKa value of the titratable residue and a positively charged amino acid reduces the pKa value. Phytase protein sequence comparisons indicate that the enzyme with acidic optimal pH has more positively charged amino acids in the substrate binding site, which gives a more favorable environment for substrate binding at low pH by providing more ionized groups in the binding site. In addition, the pH profile of phytase is affected by substrate or buffer.